We don't have experience with Waldorf, but we do have experience with a church-based preschool, which became problematic since we are not religious. I felt uncomfortable about some of the things DS was learning, since we as parents didn't believe in it. It's funny, because I specifically asked before we signed up if the preschool incorporated a lot of religion, and I was told that no, the preschool just happened to be housed in a church, and was very light on religion. And to the teacher, it probably was "very light", just not to us. And I really liked the teacher personally, and had no way to gauge this big difference until, for example, kiddo came home with what he called "the God book", which he disliked very much because it involved painting, his least favorite activity. The unfortunate side effect of a religious school with projects that the kid hated was that the kid became anti-church for awhile, associating craft projects with churches, even though we tried to stress acceptance of all different belief systems.
From what you've said, it sounds like you might face some conflict in ideologies at the Waldorf school. But if you know the director very well, maybe this won't occur. And really not trying to get into a conversation about religion, just thought I'd share an example about clash of belief systems and the effects on young people and their families.
